April 2017 - IMP-users

IMP 2.7.0 release
by Ben Webb 13 Apr '17

13 Apr '17

IMP 2.7.0 is now available. This is a bugfix and major update release. Most notably we include a preview of mmCIF support for deposition of integrative models in PDB-dev (https://pdb-dev.rcsb.rutgers.edu/) see the IMP::pmi::mmcif module for more details. This release also includes a number of bug fixes and performance improvements. Note that this will be the last release that includes packages for RedHat Enterprise Linux 5 (and variants, such as CentOS 5), since RHEL 5 has reached end of life. See https://integrativemodeling.org/2.7.0/doc/manual/changelog.html for the full change log. Check it out at https://integrativemodeling.org/ Ben -- ben(a)salilab.org https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle

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Packing group of spheres
by Dushyant Sahoo 12 Apr '17

12 Apr '17

Dear users, I am new to IMP. I am trying to pack a group of spheres inside a box. The spheres inside each group have a fixed distance from its immediate neighboring spheres. I am able to pack spheres with the constraint that spheres inside a group have a minimum distance from all other spheres. I would be really grateful if somebody could help me with this as I have a deadline coming soon. Thank You, Dushyant Sahoo

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RNA-protein crosslinking
by Genis Valentin 12 Apr '17

12 Apr '17

I would like to add a protein-RNA cross-link restraint to my representation. Is this possible at all in IMP? I tried to use a csv file similar to polii_juri.csv which is given in the IMP tutorial (https://integrativemodeling.org/2.6.2/doc/manual/rnapolii_stalk.html) prot1,res1,prot2,res2 RNA_component,345,protein_component,49 But this failes when I read it with IMP.pmi.restraints.crosslinking.ISDCrossLinkMS ISDCrossLinkMS: WARNING> residue 345 of chain RNA_component is not there Nevertheless, if I run: list_of_residues=[(345,"RNA_component")] for res in list_of_residues: particles=IMP.pmi.tools.select(representation,resolution=10,name=res[1],residue=res[0]) if len(particles)>1 : print(res[0],res[1],"more that one particle selected"); continue if len(particles)==0 : print (res[0],res[1],"no particle was selected"); continue print(res[0],res[1],IMP.core.XYZR(particles[0]).get_radius()) I get: 345 RNA_component 10.307014164455413 Thanks in advance! Genis

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rmf trajectory
by Julian 12 Apr '17

12 Apr '17

Dear IMP, I ran ReplicaExchange on multiple CPU's with MPI and have all the rmfs and logs in the output dir. I would like to recreate the simulation trajectory in a single rmf in the order that the conformations were scored. Is there a way to dig that order information out of the log files somehow? Thanks, Julian

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